Thra thyroid hormone receptor alpha [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Thraprovided by RGD
Official Full Name: thyroid hormone receptor alphaprovided by RGD
Primary source: RGD:3857
See related: Ensembl:ENSRNOG00000009066 AllianceGenome:RGD:3857
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: ERBA1; Thra1; c-erbA-1
Summary: Enables DNA-binding transcription factor activity, RNA polymerase II-specific; nucleic acid binding activity; and protein homodimerization activity. Involved in several processes, including animal organ development; digestive tract development; and regulation of transcription, DNA-templated. Located in cytosol; mitochondrion; and nucleus. Human ortholog(s) of this gene implicated in congenital nongoitrous hypothyroidism 6 and renal cell carcinoma. Orthologous to human THRA (thyroid hormone receptor alpha). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 397.8), Lung (RPKM 206.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q31

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (84198141..84225659)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (83701885..83729408)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (86657285..86684935)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Thyroid Hormone Signaling in Embryonic Stem Cells: Crosstalk with the Retinoic Acid Pathway.
Title: Thyroid Hormone Signaling in Embryonic Stem Cells: Crosstalk with the Retinoic Acid Pathway.
Alteration of thyroid hormone signaling triggers the diabetes-induced pathological growth, remodeling, and dedifferentiation of podocytes.
Title: Alteration of thyroid hormone signaling triggers the diabetes-induced pathological growth, remodeling, and dedifferentiation of podocytes.
This study demonstrated that reduction of the thyroid hormone receptor alfa (Tralpha1)mRNA expression in hippocampus of thyroidectomized Wistar rats.
Title: Antidepressant behavior in thyroidectomized Wistar rats is induced by hippocampal hypothyroidism.
The roles of nitric oxide synthase and TRalph1 in hyperthyroid and hypothyroid rats are reported.
Title: Nitric oxide and thyroid hormone receptor alpha 1 contribute to ovarian follicular development in immature hyper- and hypo-thyroid rats.
down-regulated in hepatocellular carcinoma
Title: Local hypothyroidism favors the progression of preneoplastic lesions to hepatocellular carcinoma in rats.
role for TRalpha1 in the regulation of hypothalamic TRH mRNA expression, whereas TRbeta plays a dominant role in pituitary and liver thyroid hormone metabolism.
Title: Action of specific thyroid hormone receptor α(1) and β(1) antagonists in the central and peripheral regulation of thyroid hormone metabolism in the rat.
conjugation of SUMO to TR has a TR-isoform preference and is important for T3-dependent gene induction and repression.
Title: Thyroid hormone receptor isoform-specific modification by small ubiquitin-like modifier (SUMO) modulates thyroid hormone-dependent gene regulation.
Data show that acute T3-limiting effect on reperfusion injury is mediated, at least in part, via TRalpha1 receptor.
Title: Acute T3 treatment protects the heart against ischemia-reperfusion injury via TRα1 receptor.
Data show that thyroid hormone induced rat aorta smooth muscle cell proliferation by up-regulating NOX1 in a TRalpha1-dependent manner.
Title: Thyroid hormone induces artery smooth muscle cell proliferation: discovery of a new TRalpha1-Nox1 pathway.
Acute myocardial infarction in diabetic rats results in TH receptor down-regulation with important physiological consequences
Title: Thyroid hormone can favorably remodel the diabetic myocardium after acute myocardial infarction.

Submit: New GeneRIF Correction See all GeneRIFs (28)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC64989P2 (e-PCR)
- UniSTS:273426

D17S1644E (e-PCR)
- UniSTS:147478

NR1D1_2626 (e-PCR)
- UniSTS:280871

AW259572 (e-PCR)
- UniSTS:180310

RH133144 (e-PCR)
- UniSTS:216427

Thra (e-PCR), detects polymorphism
- UniSTS:463227

MARC_26124-26125:1030369359:1 (e-PCR)
- UniSTS:268948

THRA (e-PCR), detects polymorphism
- UniSTS:279191

PMC87157P2 (e-PCR)
- UniSTS:273585

D10Got130 (e-PCR)
- UniSTS:113095

RH94515 (e-PCR)
- UniSTS:119763

RH125185 (e-PCR)
- UniSTS:162007

MARC_5497-5498:996690469:1 (e-PCR)
- UniSTS:269530

THRA_2263 (e-PCR)
- UniSTS:281056

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
NOT enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables TBP-class protein binding	IEA Inferred from Electronic Annotation more info
enables TBP-class protein binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables general transcription initiation factor binding	ISO Inferred from Sequence Orthology more info
enables intronic transcription regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear receptor activity	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	ISO Inferred from Sequence Orthology more info
enables nuclear receptor activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables steroid receptor RNA activator RNA binding	ISO Inferred from Sequence Orthology more info
enables thyroid hormone binding	IEA Inferred from Electronic Annotation more info
enables thyroid hormone binding	ISO Inferred from Sequence Orthology more info
enables thyroid hormone binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in adrenal gland development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within animal organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cartilage condensation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cartilage condensation	ISO Inferred from Sequence Orthology more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in digestive tract development	IEP Inferred from Expression Pattern more info	PubMed
involved_in embryonic organ development	IEP Inferred from Expression Pattern more info	PubMed
involved_in erythrocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within erythrocyte differentiation	ISO Inferred from Sequence Orthology more info
involved_in female courtship behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within female courtship behavior	ISO Inferred from Sequence Orthology more info
involved_in hormone-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in kidney development	IEP Inferred from Expression Pattern more info	PubMed
involved_in learning or memory	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within learning or memory	ISO Inferred from Sequence Orthology more info
involved_in liver development	IEP Inferred from Expression Pattern more info	PubMed
involved_in lung development	IEP Inferred from Expression Pattern more info	PubMed
involved_in mRNA transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription initiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of RNA polymerase II transcription preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of RNA polymerase II transcription preinitiation complex assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within ossification	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cold-induced thermogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in positive regulation of female receptivity	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of female receptivity	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of myotube differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of thyroid hormone mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of heart contraction	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of heart contraction	ISO Inferred from Sequence Orthology more info
involved_in regulation of lipid catabolic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of lipid catabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of myeloid cell apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of myeloid cell apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of thyroid hormone mediated signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of thyroid hormone mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to cold	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to cold	ISO Inferred from Sequence Orthology more info
involved_in response to nutrient levels	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in retinoic acid receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in thyroid gland development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within thyroid gland development	ISO Inferred from Sequence Orthology more info
involved_in thyroid hormone mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in type I pneumocyte differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within type I pneumocyte differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IBA Inferred from Biological aspect of Ancestor more info
part_of RNA polymerase II transcription regulator complex	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: thyroid hormone receptor alpha; c-erbAalpha2

Names: C-erbA-alpha; avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1; c-erb-A thyroid hormone receptor; c-erbA-alpha2; nuclear receptor subfamily 1 group A member 1; thyroid hormone receptor alpha 1 (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 1 formerly ERBA1)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001017960.2 → NP_001017960.1 thyroid hormone receptor alpha isoform TRalpha1

See identical proteins and their annotated locations for NP_001017960.1

Status: VALIDATED

Description

Transcript Variant: This variant (TRalpha1) differs in the 3' UTR and coding region compared to TRalpha2, resulting in a shorter isoform (TRalpha1) with a distinct C-terminus. The TRalpha1 isoform, also known as c-erbAalpha1, functions as a thyroid hormone-dependent transcription factor.

Source sequence(s)

JAXUCZ010000010

UniProtKB/TrEMBL

A0A8I6AIY7, A6HIU4

Related

ENSRNOP00000072739.1, ENSRNOT00000087346.2

Conserved Domains (2) summary

cd06935
Location:162 → 404

NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

cd06961
Location:52 → 138

NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers
NM_031134.2 → NP_112396.2 c-erbAalpha2 isoform TRalpha2

See identical proteins and their annotated locations for NP_112396.2

Status: VALIDATED

Description

Transcript Variant: This variant (TRalpha2) contains an alternate 3' terminal exon compared to variant TRalpha1. The resulting protein (c-erbAalpha2, also known as TRalpha 2) has a distinct C-terminus compared to isoform TRalpha1, and fails to bind thyroid hormones or to trans-activate thyroid hormone responsive genes.

Source sequence(s)

AI764185, CB580585, M31174

UniProtKB/Swiss-Prot

P63059

UniProtKB/TrEMBL

A6HIU2

Related

ENSRNOP00000012340.3, ENSRNOT00000012340.4

Conserved Domains (2) summary

cd06935
Location:162 → 370

NR_LBD_TR; The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

cd06961
Location:52 → 138

NR_DBD_TR; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers